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10th Anniversary of Proteomes—Reviewing the Progress and Prospects of...
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10th Anniversary of Proteomes—Reviewing the Progress and Prospects of Proteomics

A special issue of Proteomes (ISSN 2227-7382).

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 13378

Special Issue Editors

Dr. Matthew P. Padula

E-Mail Website
Guest Editor
School of Life Sciences and Proteomics Core Facility, Faculty of Science, The University of Technology Sydney, Ultimo 2007, Australia
Interests: high-resolution discovery proteomics; methodology development; top-down proteomics; two-dimensional gel electrophoresis; 2DE/MS/MS; proteoforms; lipidomics; metabolomics; data-independent acquisition
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Jens R. Coorssen

E-Mail Website
Guest Editor
1. Department of Biological Sciences, Faculty of Mathematics and Science, Brock University, St. Catharines, ON L2S 3A1, Canada
2. Ronin Institute, Montclair, NJ 07043, USA
3. Institute for Globally Distributed Open Research and Education (IGDORE), Catharines, ON L2S 3A1, Canada
Interests: analytical proteomics; high-resolution discovery proteomics; top-down proteomics; two-dimensional gel electrophoresis; 2DE/MS/MS; proteoforms/protein species; molecular mechanisms; biomarkers; membrane proteomes; synaptic function; lipidomics; metabolomics; translational proteomics; systems biology; exocytosis; preterm labor; spinal cord injury; neurodegenerative disorders
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The year 2023 marks the 10-year anniversary of Proteomes (ISSN 2227-7382), an open access, peer reviewed journal focused on all aspects of proteome analysis with a special focus on the quantification and characterisation of the proteome at the level of proteoforms. Proteomes was indexed in Emerging Sources Citation Index (ESCI), Web of Science (Clarivate Analytics) in 2016 before being indexed by Scopus and PubMed in 2017 and receiving its first CiteScore (2017) of 2.3 in 2018. In 2023, its 10th anniversary year, Proteomes will receive its first Impact Factor, which we expect to place the journal quite highly in the field.

To date, 373 articles from 1946 authors have been published in Proteomes, with 140 of these articles being cited 10 times or more. The editors and editorial staff sincerely thank all of Proteomes readers, authors, and anonymous peer reviewers who have contributed time and effort throughout the years. Proteomes would not have been possible or successful without your participation.

To celebrate the 10th Anniversary, a Special Issue is being launched that reflects on the last ten years of Proteomes and proteomics to discuss what the field has achieved and what needs to be achieved for proteomics as a discipline to provide the desperately needed breakthroughs required in medicine and biotechnology. Sections editors have been asked to provide reviews, but we invite contributions from the broader scientific community for peer review and potential publication.

Dr. Matthew P. Padula
Prof. Dr. Jens R. Coorssen
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (i.e., as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except as conference abstracts). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Authors are encouraged to thoroughly familiarize themselves with the expectations of the journal before committing to submission and publication. Proteomes is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript; again, authors are encouraged to thoroughly familiarize themselves with the expectations of the journal. The Article Processing Charge (APC) for publication in this open access journal is 1600 CHF (Swiss Francs). Submitted papers should be well formatted and use proper English. Authors may use MDPI's English editing service prior to publication or during author revisions.

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Published Papers (5 papers)

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32 pages, 6256 KiB  
Article
Cadmium Highlights Common and Specific Responses of Two Freshwater Sentinel Species, Dreissena polymorpha and Dreissena rostriformis bugensis
by Florence Bultelle, Aimie Le Saux, Elise David, Arnaud Tanguy, Simon Devin, Stéphanie Olivier, Agnès Poret, Philippe Chan, Fanny Louis, Laurence Delahaut, Sandrine Pain-Devin, Romain Péden, David Vaudry, Frank Le Foll and Béatrice Rocher
Proteomes 2024, 12(2), 10; https://doi.org/10.3390/proteomes12020010 - 26 Mar 2024
Viewed by 1842
Abstract
Zebra mussel (ZM), Dreissena polymorpha, commonly used as a sentinel species in freshwater biomonitoring, is now in competition for habitat with quagga mussel (QM), Dreissena rostriformis bugensis. This raises the question of the quagga mussel’s use in environmental survey. To better characterise [...] Read more.
Zebra mussel (ZM), Dreissena polymorpha, commonly used as a sentinel species in freshwater biomonitoring, is now in competition for habitat with quagga mussel (QM), Dreissena rostriformis bugensis. This raises the question of the quagga mussel’s use in environmental survey. To better characterise QM response to stress compared with ZM, both species were exposed to cadmium (100 µg·L−1), a classic pollutant, for 7 days under controlled conditions. The gill proteomes were analysed using two-dimensional electrophoresis coupled with mass spectrometry. For ZM, 81 out of 88 proteoforms of variable abundance were identified using mass spectrometry, and for QM, 105 out of 134. Interestingly, the proteomic response amplitude varied drastically, with 5.6% of proteoforms of variable abundance (DAPs) in ZM versus 9.4% in QM. QM also exhibited greater cadmium accumulation. Only 12 common DAPs were observed. Several short proteoforms were detected, suggesting proteolysis. Functional analysis is consistent with the pleiotropic effects of the toxic metal ion cadmium, with alterations in sulphur and glutathione metabolisms, cellular calcium signalling, cytoskeletal dynamics, energy production, chaperone activation, and membrane events with numerous proteins involved in trafficking and endocytosis/exocytosis processes. Beyond common responses, the sister species display distinct reactions, with cellular response to stress being the main category involved in ZM as opposed to calcium and cytoskeleton alterations in QM. Moreover, QM exhibited greater evidence of proteolysis and cell death. Overall, these results suggest that QM has a weaker stress response capacity than ZM. Full article
(This article belongs to the Special Issue 10th Anniversary of Proteomes—Reviewing the Progress and Prospects of Proteomics)
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14 pages, 2376 KiB  
Article
Observations from the Proteomics Bench
by Simone König, Karin Schork and Martin Eisenacher
Proteomes 2024, 12(1), 6; https://doi.org/10.3390/proteomes12010006 - 6 Feb 2024
Cited by 1 | Viewed by 2002
Abstract
Many challenges in proteomics result from the high-throughput nature of the experiments. This paper first presents pre-analytical problems, which still occur, although the call for standardization in omics has been ongoing for many years. This article also discusses aspects that affect bioinformatic analysis [...] Read more.
Many challenges in proteomics result from the high-throughput nature of the experiments. This paper first presents pre-analytical problems, which still occur, although the call for standardization in omics has been ongoing for many years. This article also discusses aspects that affect bioinformatic analysis based on three sets of reference data measured with different orbitrap instruments. Despite continuous advances in mass spectrometer technology as well as analysis software, data-set-wise quality control is still necessary, and decoy-based estimation, although challenged by modern instruments, should be utilized. We draw attention to the fact that numerous young researchers perceive proteomics as a mature, readily applicable technology. However, it is important to emphasize that the maximum potential of the technology can only be realized by an educated handling of its limitations. Full article
(This article belongs to the Special Issue 10th Anniversary of Proteomes—Reviewing the Progress and Prospects of Proteomics)
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15 pages, 2884 KiB  
Perspective
Puzzle of Proteoform Variety—Where Is a Key?
by Stanislav Naryzhny
Proteomes 2024, 12(2), 15; https://doi.org/10.3390/proteomes12020015 - 10 May 2024
Viewed by 1518
Abstract
One of the human proteome puzzles is an imbalance between the theoretically calculated and experimentally measured amounts of proteoforms. Considering the possibility of combinations of different post-translational modifications (PTMs), the quantity of possible proteoforms is huge. An estimation gives more than a million [...] Read more.
One of the human proteome puzzles is an imbalance between the theoretically calculated and experimentally measured amounts of proteoforms. Considering the possibility of combinations of different post-translational modifications (PTMs), the quantity of possible proteoforms is huge. An estimation gives more than a million different proteoforms in each cell type. But, it seems that there is strict control over the production and maintenance of PTMs. Although the potential complexity of proteoforms due to PTMs is tremendous, available information indicates that only a small part of it is being implemented. As a result, a protein could have many proteoforms according to the number of modification sites, but because of different systems of personal regulation, the profile of PTMs for a given protein in each organism is slightly different. Full article
(This article belongs to the Special Issue 10th Anniversary of Proteomes—Reviewing the Progress and Prospects of Proteomics)
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24 pages, 412 KiB  
Perspective
Proteomics—The State of the Field: The Definition and Analysis of Proteomes Should Be Based in Reality, Not Convenience
by Jens R. Coorssen and Matthew P. Padula
Proteomes 2024, 12(2), 14; https://doi.org/10.3390/proteomes12020014 - 19 Apr 2024
Cited by 2 | Viewed by 3918
Abstract
With growing recognition and acknowledgement of the genuine complexity of proteomes, we are finally entering the post-proteogenomic era. Routine assessment of proteomes as inferred correlates of gene sequences (i.e., canonical ‘proteins’) cannot provide the necessary critical analysis of systems-level biology that is needed [...] Read more.
With growing recognition and acknowledgement of the genuine complexity of proteomes, we are finally entering the post-proteogenomic era. Routine assessment of proteomes as inferred correlates of gene sequences (i.e., canonical ‘proteins’) cannot provide the necessary critical analysis of systems-level biology that is needed to understand underlying molecular mechanisms and pathways or identify the most selective biomarkers and therapeutic targets. These critical requirements demand the analysis of proteomes at the level of proteoforms/protein species, the actual active molecular players. Currently, only highly refined integrated or integrative top-down proteomics (iTDP) enables the analytical depth necessary to provide routine, comprehensive, and quantitative proteome assessments across the widest range of proteoforms inherent to native systems. Here we provide a broad perspective of the field, taking in historical and current realities, to establish a more balanced understanding of where the field has come from (in particular during the ten years since Proteomes was launched), current issues, and how things likely need to proceed if necessary deep proteome analyses are to succeed. We base this in our firm belief that the best proteomic analyses reflect, as closely as possible, the native sample at the moment of sampling. We also seek to emphasise that this and future analytical approaches are likely best based on the broad recognition and exploitation of the complementarity of currently successful approaches. This also emphasises the need to continuously evaluate and further optimize established approaches, to avoid complacency in thinking and expectations but also to promote the critical and careful development and introduction of new approaches, most notably those that address proteoforms. Above all, we wish to emphasise that a rigorous focus on analytical quality must override current thinking that largely values analytical speed; the latter would certainly be nice, if only proteoforms could thus be effectively, routinely, and quantitatively assessed. Alas, proteomes are composed of proteoforms, not molecular species that can be amplified or that directly mirror genes (i.e., ‘canonical’). The problem is hard, and we must accept and address it as such, but the payoff in playing this longer game of rigorous deep proteome analyses is the promise of far more selective biomarkers, drug targets, and truly personalised or even individualised medicine. Full article
(This article belongs to the Special Issue 10th Anniversary of Proteomes—Reviewing the Progress and Prospects of Proteomics)
41 pages, 4798 KiB  
Perspective
How Can Proteomics Help to Elucidate the Pathophysiological Crosstalk in Muscular Dystrophy and Associated Multi-System Dysfunction?
by Paul Dowling, Capucine Trollet, Elisa Negroni, Dieter Swandulla and Kay Ohlendieck
Proteomes 2024, 12(1), 4; https://doi.org/10.3390/proteomes12010004 - 16 Jan 2024
Cited by 1 | Viewed by 3379
Abstract
This perspective article is concerned with the question of how proteomics, which is a core technique of systems biology that is deeply embedded in the multi-omics field of modern bioresearch, can help us better understand the molecular pathogenesis of complex diseases. As an [...] Read more.
This perspective article is concerned with the question of how proteomics, which is a core technique of systems biology that is deeply embedded in the multi-omics field of modern bioresearch, can help us better understand the molecular pathogenesis of complex diseases. As an illustrative example of a monogenetic disorder that primarily affects the neuromuscular system but is characterized by a plethora of multi-system pathophysiological alterations, the muscle-wasting disease Duchenne muscular dystrophy was examined. Recent achievements in the field of dystrophinopathy research are described with special reference to the proteome-wide complexity of neuromuscular changes and body-wide alterations/adaptations. Based on a description of the current applications of top-down versus bottom-up proteomic approaches and their technical challenges, future systems biological approaches are outlined. The envisaged holistic and integromic bioanalysis would encompass the integration of diverse omics-type studies including inter- and intra-proteomics as the core disciplines for systematic protein evaluations, with sophisticated biomolecular analyses, including physiology, molecular biology, biochemistry and histochemistry. Integrated proteomic findings promise to be instrumental in improving our detailed knowledge of pathogenic mechanisms and multi-system dysfunction, widening the available biomarker signature of dystrophinopathy for improved diagnostic/prognostic procedures, and advancing the identification of novel therapeutic targets to treat Duchenne muscular dystrophy. Full article
(This article belongs to the Special Issue 10th Anniversary of Proteomes—Reviewing the Progress and Prospects of Proteomics)
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